RetrogeneDB ID: retro_etel_1701

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_288242:56031..56490(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ZNHIT1
• Ensembl ID: ENSETEG00000010174
• Aliases: None
• Description: zinc finger, HIT-type containing 1 [Source:HGNC Symbol;Acc:21688]

Sequence

>retro_etel_1701
GAAGAGATCACTTCCGCTTCTTCCCAGGATACCAGACAGTGGTGGATGCTGGACCTGGTAGCCACGCAGCGCAGCATCAA
GAGACAGCTTGCAGCATTGGAGAAAGGTGGCTTCCAAGAAAACCGTCATGCAGGACTCCCTCAGCTCAACGAGAGACTGT
CTCAGTTGGATGCTGATAGAGATGCCAGAAAGAAAAAGGAGAAAACATGAGATCATTTTAAACTTCTCCTTTACTTCAGG
AAAAACCTATCAAGCCCTATTGAAGGAGCAAAACTTGAGAGTGGTCAAGTGAACCAATTACCCAACAGCCTGTGTCAGAA
GCCCCTCCAGGACCCACGGCCCCTTCTGTGCTGTCTCTGGCTTCCCCTCCCCATACACCTGTGTCAGCTGTGGTGCCTGG
TATTGCACCATGTGTGTCTGGGTACCCAACAGGCCAGCGGGTGCATGAAGTGGACTCTG

Alignment

ORF - retro_etel_1701 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.26 %
• Parental protein coverage: 98.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKKASFRSQDPGQRRVLDRAARQRRINRQLEALENDNFQDDPHAGLPQLGKRLPQFDDDTDTGKKKKKTR
          E...S..SQD..Q...LD..A.QR.I.RQL.ALE...FQ...HAGLPQL..RL.Q.D.D.D..KKK.KT.
Retrocopy EEITSASSQDTRQWWMLDLVATQRSIKRQLAALEKGGFQENRHAGLPQLNERLSQLDADRDARKKKEKT*

Parental  GDHFKLR--FRKN-FQALLEEQNLSVAEGPNYLTACAGPPSRPQRPFCAVCGFPSPYTCVSCGARYCTV-
          .DHFKL...FRKN..QALL.EQNL.V....NY.TAC...PSR...PFCAV.GFPSPYTCVSCGA.YCT..
Retrocopy -DHFKLLLYFRKN>YQALLKEQNLRVVK*TNYPTACVRSPSRTHGPFCAVSGFPSPYTCVSCGAWYCTM<

Parental  RCLGTHQETRCLKWTV
          .CLGT.Q...C.KWT.
Retrocopy VCLGTQQASGCMKWTL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_1701 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000010174	1 retrocopy	retro_etel_1701 ,
Homo sapiens	ENSG00000106400	1 retrocopy	retro_hsap_4012,
Gorilla gorilla	ENSGGOG00000016713	1 retrocopy	retro_ggor_2694,
Macaca mulatta	ENSMMUG00000006951	1 retrocopy	retro_mmul_2315,
Pan troglodytes	ENSPTRG00000019525	1 retrocopy	retro_ptro_2723,
Rattus norvegicus	ENSRNOG00000001418	2 retrocopies	retro_rnor_2162, retro_rnor_2278,